PDB-2bgy: FIT OF THE X-RAY STRUCUTRE OF THE BATERIAL FLAGELLAR HO... - EM Navigator

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FIT OF THE X-RAY STRUCUTRE OF THE BATERIAL FLAGELLAR HOOK FRAGMENT FLGE31 INTO AN EM MAP FROM THE HOOK OF CAULOBACTER CRESCENTUS.

by electron crystallography, at 20 A resolution

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#1: Depositted structure unit, Made by Jmol

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 2bgy
Title	FIT OF THE X-RAY STRUCUTRE OF THE BATERIAL FLAGELLAR HOOK FRAGMENT FLGE31 INTO AN EM MAP FROM THE HOOK OF CAULOBACTER CRESCENTUS.
Descriptor	FLAGELLAR HOOK PROTEIN FLGE
Keywords	MOTOR PROTEIN, BACTERIAL MOTILITY, FLAGELLAR HOOK, FLAGELLUM
Authors	Shaikh, T.R., Thomas, D.R., Chen, J.Z., Samatey, F.A., Matsunami, H., Imada, K., Namba, K., Derosier, D.J.
Date	Deposition: 2005-01-06, Release: 2005-01-27
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1132 CiteFit PDB-2bgz Cite PDB-1wlg Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-2bgz EMDB-1916 PDB-3cre PDB-3crf List of similar structure data about Omokage system

Article
Citation - primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 102, Issue 4, Page 1023-8, Year 2005
Title	A partial atomic structure for the flagellar hook of Salmonella typhimurium.
Authors	Tanvir R Shaikh, Dennis R Thomas, James Z Chen, Fadel A Samatey, Hideyuki Matsunami, Katsumi Imada, Keiichi Namba, David J Derosier Dynamic NanoMachine Project, International Cooperative Research Project, Japan Science and Technology Agency, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
Keywords	Amino Acid Sequence, Bacterial Proteins (chemistry), Models, Molecular, Molecular Sequence Data, Protein Structure, Secondary, Salmonella typhimurium (chemistry), hook protein, bacterial flagellum
Links	DOI: 10.1073/pnas.0409020102, PubMed: 15657146, PMC: PMC545859
Citation - 1
Article	Nature, Vol. 431, Issue 7012, Page 1062-8, Year 2004
Title	Structure of the bacterial flagellar hook and implication for the molecular universal joint mechanism.
Authors	Fadel A Samatey, Hideyuki Matsunami, Katsumi Imada, Shigehiro Nagashima, Tanvir R Shaikh, Dennis R Thomas, James Z Chen, David J Derosier, Akio Kitao, Keiichi Namba Dynamic NanoMachine Project, ICORP, JST, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
Keywords	Bacterial Proteins (chemistry), Computer Simulation, Cryoelectron Microscopy, Crystallography, X-Ray, FlgE protein, Bacteria, Models, Molecular, Peptide Fragments (chemistry), Pliability, Protein Structure, Quaternary, Protein Subunits (chemistry), Salmonella typhimurium (chemistry)
Links	DOI: 10.1038/nature02997, PubMed: 15510139

Components
ID 1 : FLAGELLAR HOOK PROTEIN FLGE
Image
Description	FLAGELLAR HOOK PROTEIN FLGE
Type	polymer
Fragment	FLGE31 RESIDUES 71-363
Formula weight	31335.338 Da
Number of molecules	1
Source	Method: Isolated from a genetically manipulated source Gene: ID:602, SALMONELLA TYPHIMURIUM Host: ID:562, ESCHERICHIA COLI
Links	UniProt: P16322, Sequence view

Sample
Assembly
Aggregation state	2D CRYSTAL
Name	POLYHOOK
Buffer
Name	10 MM TRIS/HCL,5MM EDTA,0. 1%V/V TRITON X-100
Experiment
Reconstruction method	CRYSTALLOGRAPHY
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	8.0
Sample support
Details	HOLEY CARBON
Vitrification
Details	SAMPLES PREPARED AT 4 DEG C PLUNGED INTO LIQUID ETHANE

Electron Microscopy
Imaging
Microscope	model: FEI CM200 FEG
Electron gun
Electron source	FEG
Accelerating voltage	200 kV
Illumination mode	LOW DOSE
Lens
Mode	BRIGHT FIELD
Detector
Type	KODAK SO-163 FILM

Processing
2D projection selection
Software name	RSREF
3D reconstruction
Details	FIT OF S. TYPHIMURIUM HOOK CRYSTAL STRUCTURE PDB ID 1WLG INTO AN EM MAP OF HOOK FROM C. CRESCENTUS
Refine
Ls d res high	20.00 A
ID	1
Refine hist
D res high	20.00
Total atoms	2156
Protein atoms	2156

PDB format

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mmCIF

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2bgy-noatom.xml.gz

Ext-atom

2bgy-extatom.xml.gz

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 2.4 MB .webm (WebM/VP8 format), 3.4 MB